Hotfix

buildContainers.nf

@@ -36,7 +36,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.1'
+version = '1.2.2'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented

buildReferences.nf

@@ -39,7 +39,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.1'
+version = '1.2.2'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented

configuration/uppmax-localhost.config

@@ -60,31 +60,31 @@ process {
     memory = {params.totalMemory}
   }
   $IndelRealigner {
-    memory = params.singleCPUMem * 2 * task.attempt
+    memory = {params.singleCPUMem * 2 * task.attempt}
   }
   $MapReads {
     cpus = 16
     memory = {params.totalMemory}
   }
   $MarkDuplicates {
-    memory = params.singleCPUMem * 2 * task.attempt
+    memory = {params.singleCPUMem * 2 * task.attempt}
   }
   $MergeBams {
     cpus = 16
     memory = {params.totalMemory}
   }
   $RealignerTargetCreator {
     cpus = 4
-    memory = params.singleCPUMem * 4 * task.attempt
+    memory = {params.singleCPUMem * 4 * task.attempt}
   }
   $RecalibrateBam {
     memory = {params.singleCPUMem * task.attempt}
   }
   $RunAlleleCount {
-    memory = params.singleCPUMem * 2 * task.attempt
+    memory = {params.singleCPUMem * 2 * task.attempt}
   }
   $RunAscat {
-    memory = params.singleCPUMem * 2 * task.attempt
+    memory = {params.singleCPUMem * 2 * task.attempt}
   }
   $RunBamQC {
     cpus = 16
@@ -93,18 +93,18 @@ process {
   $RunBcftoolsStats {
   }
   $RunConvertAlleleCounts {
-    memory = params.singleCPUMem * 2 * task.attempt
+    memory = {params.singleCPUMem * 2 * task.attempt}
   }
   $RunFastQC {
-    errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
+    errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
   $RunFreeBayes {
     cpus = 1
-    memory = { params.singleCPUMem * task.attempt}
+    memory = {params.singleCPUMem * task.attempt}
   }
   $RunHaplotypecaller {
     // Increase memory quadratically
-    memory = params.singleCPUMem * task.attempt * task.attempt
+    memory = {params.singleCPUMem * task.attempt * task.attempt}
   }
   $RunGenotypeGVCFs {
   }
@@ -116,24 +116,24 @@ process {
   }
   $RunMutect1 {
     cpus = 1
-    memory = { params.singleCPUMem * task.attempt}
+    memory = {params.singleCPUMem * task.attempt}
   }
   $RunMutect2 {
     cpus = 1
-    memory = { params.singleCPUMem * task.attempt}
+    memory = {params.singleCPUMem * task.attempt}
   }
   $RunSamtoolsStats {
   }
   $RunSnpeff {
-    errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
+    errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
     memory = {params.totalMemory} // TODO Does SnpEff really require that much?
   }
   $RunStrelka {
     cpus = 16
     memory = {params.totalMemory}
   }
   $RunVEP {
-    errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
+    errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
     memory = {params.totalMemory} // TODO Does VEP really require that much?
   }
 }

main.nf

@@ -63,7 +63,7 @@ kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 */
 
-version = '1.2.1'
+version = '1.2.2'
 
 // Check that Nextflow version is up to date enough
 // try / throw / catch works for NF versions < 0.25 when this was implemented